GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACT - ACT domain
Pfam: PF01842 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0070
Length: 66
Sequences: 12914
Seq/Len: 195.67
HH_delta: 0.041 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
24_H60_E2.045393.148
19_E23_D1.833742.822
15_A19_E1.727522.659
21_L26_I1.531192.357
7_V13_I1.401222.157
58_L62_E1.364122.100
55_E59_E1.06871.645
14_L18_T1.058981.630
24_H56_K1.058171.629
15_A22_A1.052011.619
20_I60_E0.963031.482
14_L31_I0.950811.463
23_D60_E0.94721.458
5_V17_V0.944831.454
53_D56_K0.909071.399
20_I23_D0.86791.336
13_I16_D0.859741.323
18_T28_I0.840411.294
16_D19_E0.84031.293
10_R16_D0.785621.209
20_I24_H0.783341.206
59_E62_E0.774631.192
56_K59_E0.755331.163
60_E63_A0.753491.160
4_R43_V0.750851.156
49_V53_D0.748711.152
50_D53_D0.747911.151
56_K60_E0.736931.134
15_A18_T0.722671.112
59_E63_A0.716951.104
29_D47_I0.710281.093
16_D22_A0.705611.086
32_S45_I0.687561.058
11_P25_G0.675031.039
19_E22_A0.669361.030
10_R13_I0.633410.975
6_I41_G0.631780.972
9_D12_G0.567010.873
11_P27_N0.566440.872
33_Q42_I0.56610.871
55_E58_L0.564050.868
9_D27_N0.554670.854
18_T22_A0.552380.850
12_G27_N0.552260.850
44_F47_I0.546540.841
16_D20_I0.543320.836
32_S43_V0.536630.826
30_S48_V0.523050.805
34_S42_I0.512290.789
4_R41_G0.50930.784
54_L57_L0.502110.773
52_E56_K0.499290.769
51_E54_L0.497870.766
46_V49_V0.492470.758
27_N47_I0.475190.731
26_I57_L0.474890.731
11_P22_A0.440790.678
37_K40_V0.431060.663
54_L58_L0.430620.663
28_I31_I0.429780.662
7_V31_I0.42910.660
36_D41_G0.420260.647
42_I47_I0.418890.645
36_D43_V0.41860.644
42_I46_V0.416370.641
26_I53_D0.415080.639
7_V14_L0.414480.638
18_T31_I0.408920.629
20_I61_L0.407480.627
57_L61_L0.404940.623
18_T21_L0.397670.612
34_S37_K0.393580.606
42_I45_I0.392230.604
21_L57_L0.389140.599
50_D54_L0.388450.598
43_V46_V0.381780.588
31_I35_S0.377060.580
35_S38_D0.373710.575
23_D63_A0.372160.573
30_S33_Q0.37120.571
30_S45_I0.365390.562
51_E55_E0.35220.542
9_D35_S0.35110.540
21_L44_F0.350020.539
12_G16_D0.346850.534
22_A27_N0.343320.528
5_V13_I0.339360.522
41_G45_I0.337520.520
7_V33_Q0.337220.519
34_S43_V0.336120.517
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2lvwA197.50.041
2ko1A197.50.045
1zpvA197.40.062
3p96A197.40.071
3n0vA197.30.086
3mtjA197.20.105
3o1lA197.20.109
3louA197.20.11
2nyiA0.984897.20.117
2f1fA197.10.123

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